I have the same issue. From ArcMap I build a definition query to display only items tagged with "Active" out of a total of 4 subtypes.
I published the dataset to the server and imported to ArcGIS Online webmap. It displays on the map only Active projects, however the legend contains all the subtypes, even though I only want to see Active.
I do not want to save out Active projects and publish because I'm pulling data from an SDE where the data is always being updated and I need the most current data displayed.
I just don't want to see the other subtypes in the Legend.
Ideas?